PyORCA.geometry reference

Simple geometric functions

pyorca.geometry.distance(coords1: List[float], coords2: List[float]) → float

Returns euclidean distance between the two points

pyorca.geometry.angle_degree(coords1: List[float], coords2: List[float], coords3: List[float]) → float

Returns the angle in degrees defined by the three points

pyorca.geometry.dihedral_degree(coords1: List[float], coords2: List[float], coords3: List[float], coords4: List[float]) → float

Returns the dihedral angle in degrees defined by the four points

Aligning structures

pyorca.geometry.aligned_rmsd(coords1: List[List[float]] | array, coords2: List[List[float]] | array) → float

Aligns the structures and returns the RMSD. Assumes the ordering of atoms is identical in both.

pyorca.geometry.align_xyz_files(path1: str, path2: str) → float

Aligns molecules from .xyz files and returns the RMSD

.xyz files

pyorca.geometry.read_xyz(text: str) → Tuple[List[str], array, str]

Reads .xyz text and returns atoms, coordinates and comment line

pyorca.geometry.write_xyz(atoms: List[str], coords: List[List[float]], comment: str = '') → str

Generates .xyz text from given atoms and coords

pyorca.geometry.generate_xyz_block(atoms: List[str], coords: List[List[float]]) → str

Generates xyz block from given atoms and coords. This can be used to generate ORCA input files.